Most likely either create a new category and slowly delete the old ones, unless there's an external "old patch" version exists which will allow runs to be played.

If GSG changes cave generation, the same applies. New versions will have their own category, as old categories will be obsolete and deleted after a while.

Minor changes (like bosco upgrades from patch 20) will probably not affect the leaderboards unless the change impacts the speedruns so negatively that the WR cannot ever be beaten again.